AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene065615

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene065615.t1 MTR_6g059530 92.118 203 14 1 1 201 1 203 1.85e-123 347
MS.gene065615.t1 MTR_6g059410 89.655 203 18 2 1 201 1 202 1.42e-118 335
MS.gene065615.t1 MTR_6g059650 55.670 194 76 5 17 201 19 211 6.98e-65 199
MS.gene065615.t1 MTR_6g065460 55.340 206 77 7 1 193 1 204 2.43e-57 180
MS.gene065615.t1 MTR_6g065460 50.980 204 65 7 1 193 1 180 4.89e-48 155
MS.gene065615.t1 MTR_6g059760 48.804 209 90 11 1 196 1 205 8.88e-48 155
MS.gene065615.t1 MTR_6g044780 44.186 215 101 10 1 199 1 212 2.31e-41 140
MS.gene065615.t1 MTR_6g059680 47.525 202 87 9 16 201 18 216 2.90e-40 137
MS.gene065615.t1 MTR_3g463590 43.750 192 95 8 20 201 23 211 7.23e-40 135
MS.gene065615.t1 MTR_6g045097 43.256 215 103 10 1 199 1 212 3.52e-39 134
MS.gene065615.t1 MTR_6g044810 43.256 215 103 10 1 199 1 212 1.19e-38 132
MS.gene065615.t1 MTR_6g045403 42.523 214 104 9 1 199 1 210 4.34e-37 129
MS.gene065615.t1 MTR_6g059730 45.116 215 101 10 1 201 1 212 1.29e-36 127
MS.gene065615.t1 MTR_6g009650 41.827 208 102 9 1 194 1 203 3.52e-34 120
MS.gene065615.t1 MTR_6g066190 40.670 209 105 9 1 195 1 204 1.32e-33 119
MS.gene065615.t1 MTR_6g017225 40.187 214 106 11 6 201 7 216 1.11e-32 120
MS.gene065615.t1 MTR_6g045433 37.662 231 102 11 1 201 1 219 2.03e-32 116
MS.gene065615.t1 MTR_6g059810 39.614 207 99 9 4 190 8 208 1.16e-30 112
MS.gene065615.t1 MTR_6g009563 39.713 209 106 9 1 194 1 204 3.35e-30 110
MS.gene065615.t1 MTR_6g066210 39.151 212 114 8 1 199 1 210 4.55e-29 107
MS.gene065615.t1 MTR_1g035770 40.291 206 101 11 6 192 7 209 1.98e-26 101
MS.gene065615.t1 MTR_6g059755 49.074 108 49 4 98 199 18 125 4.58e-25 95.1
MS.gene065615.t1 MTR_6g078070 33.171 205 123 8 1 193 1 203 6.13e-20 84.0
MS.gene065615.t1 MTR_6g078100 33.654 208 120 9 1 193 1 205 6.38e-18 78.6
MS.gene065615.t1 MTR_1g057110 36.715 207 98 11 1 194 1 187 2.49e-17 76.6
MS.gene065615.t1 MTR_6g065570 55.000 60 24 1 16 72 14 73 1.11e-14 67.0
MS.gene065615.t1 MTR_0100s0150 27.861 201 127 7 5 190 1 198 3.93e-13 65.5
MS.gene065615.t1 MTR_3g106620 30.387 181 109 9 24 194 27 200 1.58e-12 64.3
MS.gene065615.t1 MTR_0302s0030 27.723 202 127 7 5 190 1 199 3.13e-12 63.2
MS.gene065615.t1 MTR_0084s0030 29.208 202 124 8 5 190 1 199 3.64e-12 63.2
MS.gene065615.t1 MTR_0211s0080 28.283 198 127 7 5 190 1 195 6.92e-12 62.0
MS.gene065615.t1 MTR_6g078290 30.732 205 112 10 11 190 10 209 1.29e-11 61.6
MS.gene065615.t1 MTR_2g073010 27.919 197 134 6 1 193 6 198 2.33e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene065615.t1 AT1G73260 34.426 183 106 7 26 197 30 209 7.31e-21 86.7
MS.gene065615.t1 AT1G17860 31.492 181 107 7 21 193 24 195 1.03e-15 72.4
MS.gene065615.t1 AT1G73325 31.220 205 126 9 4 197 7 207 3.41e-12 63.5

Find 49 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAATAGTTGAAGACATAAA+TGG 0.300956 6.3:+63743194 MS.gene065615:CDS
CAACTGAAAATAACCCCTTT+TGG 0.303854 6.3:+63743663 MS.gene065615:CDS
GGTAAGTAATGTTGGCTTCA+TGG 0.309270 6.3:-63743123 None:intergenic
ACTGTTATGGTAAATCTAAC+TGG 0.326794 6.3:-63743362 None:intergenic
ACTATTTCAGCAAAAGCTAA+TGG 0.332530 6.3:-63743179 None:intergenic
AAATCTTGTAGTACAGTAAC+TGG 0.343098 6.3:-63743317 None:intergenic
CCTGGCGCTTGTAGTGATAT+TGG 0.366872 6.3:+63743605 MS.gene065615:CDS
AAAATTGAGACAATTGGTTC+AGG 0.373759 6.3:+63743542 MS.gene065615:CDS
AATGGAAACCCCGTATTTCC+TGG 0.375075 6.3:+63743212 MS.gene065615:CDS
CCTACATCCTGGGTAGGTAT+TGG 0.376991 6.3:+63743488 MS.gene065615:CDS
AAATTTAAAATTGAGACAAT+TGG 0.414016 6.3:+63743536 MS.gene065615:CDS
GATAATATTGATGCATTTCA+AGG 0.419889 6.3:+63743512 MS.gene065615:CDS
TCAACGAATACAACCCAAAA+GGG 0.432534 6.3:-63743677 None:intergenic
AGAGAAAAGGTAAGTAATGT+TGG 0.440708 6.3:-63743131 None:intergenic
ATCTCTAAAGGAGGAGGTGG+TGG 0.449806 6.3:+63743260 MS.gene065615:CDS
GAAAGTAGGTAAAGGAAAAG+AGG 0.466771 6.3:-63743157 None:intergenic
CCAATACCTACCCAGGATGT+AGG 0.475428 6.3:-63743488 None:intergenic
ATCATGAGCTAGCACCCATT+TGG 0.477611 6.3:-63743459 None:intergenic
TGGAGATTTGATTCAAACTA+CGG 0.490153 6.3:-63743720 None:intergenic
ATGATGATTTCCCTACATCC+TGG 0.490169 6.3:+63743477 MS.gene065615:CDS
AGATAAGAATGGATGGCGTC+TGG 0.490689 6.3:+63743637 MS.gene065615:CDS
GGATTGAAGCTTGGTAAGAC+AGG 0.499062 6.3:+63743281 MS.gene065615:CDS
CCATTGTTCAGTGCTCCACC+TGG 0.501984 6.3:+63743587 MS.gene065615:CDS
ATCAACGAATACAACCCAAA+AGG 0.508809 6.3:-63743678 None:intergenic
GGAAAAGAGGAGGAGAGAAA+AGG 0.510811 6.3:-63743144 None:intergenic
GGAGGTGGTGGATTGAAGCT+TGG 0.515566 6.3:+63743272 MS.gene065615:CDS
CCTCCTCCTTTAGAGATAAG+TGG 0.523049 6.3:-63743254 None:intergenic
GTGTGCTGAATCTGCCAAAT+GGG 0.523391 6.3:+63743445 MS.gene065615:CDS
ATTGCACCACTTATCTCTAA+AGG 0.523973 6.3:+63743248 MS.gene065615:CDS
GGAAGGTATAAAGATAAGAA+TGG 0.524313 6.3:+63743626 MS.gene065615:CDS
AGTGTGCTGAATCTGCCAAA+TGG 0.527935 6.3:+63743444 MS.gene065615:CDS
TTGGCAGATTCAGCACACTT+TGG 0.530934 6.3:-63743440 None:intergenic
CAATACCTACCCAGGATGTA+GGG 0.542912 6.3:-63743487 None:intergenic
AGCAAAAGCTAATGGAAAGT+AGG 0.543819 6.3:-63743171 None:intergenic
AGCTAATGGAAAGTAGGTAA+AGG 0.547073 6.3:-63743165 None:intergenic
CCAATATCACTACAAGCGCC+AGG 0.552948 6.3:-63743605 None:intergenic
TGATGATTTCCCTACATCCT+GGG 0.571431 6.3:+63743478 MS.gene065615:CDS
CTTATCTCTAAAGGAGGAGG+TGG 0.573275 6.3:+63743257 MS.gene065615:CDS
AGTAGGTAAAGGAAAAGAGG+AGG 0.584445 6.3:-63743154 None:intergenic
GGTATAAAGATAAGAATGGA+TGG 0.584646 6.3:+63743630 MS.gene065615:CDS
CCACTTATCTCTAAAGGAGG+AGG 0.587891 6.3:+63743254 MS.gene065615:CDS
ATTATCACCAATACCTACCC+AGG 0.608189 6.3:-63743495 None:intergenic
GCGCTTGTAGTGATATTGGA+AGG 0.629705 6.3:+63743609 MS.gene065615:CDS
GATTTCCCTACATCCTGGGT+AGG 0.630370 6.3:+63743482 MS.gene065615:CDS
CCAGGTGGAGCACTGAACAA+TGG 0.632227 6.3:-63743587 None:intergenic
GCACCACTTATCTCTAAAGG+AGG 0.639013 6.3:+63743251 MS.gene065615:CDS
CAACGAATACAACCCAAAAG+GGG 0.675837 6.3:-63743676 None:intergenic
ATATCACTACAAGCGCCAGG+TGG 0.717315 6.3:-63743602 None:intergenic
TTTACCATAACAGTAAAACG+TGG 0.801296 6.3:+63743371 MS.gene065615:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATTTAAAATTGAGACAAT+TGG + chr6.3:63743536-63743555 MS.gene065615:CDS 15.0%
! GAAATAGTTGAAGACATAAA+TGG + chr6.3:63743194-63743213 MS.gene065615:CDS 25.0%
! GATAATATTGATGCATTTCA+AGG + chr6.3:63743512-63743531 MS.gene065615:CDS 25.0%
AAATCTTGTAGTACAGTAAC+TGG - chr6.3:63743320-63743339 None:intergenic 30.0%
ACTATTTCAGCAAAAGCTAA+TGG - chr6.3:63743182-63743201 None:intergenic 30.0%
ACTGTTATGGTAAATCTAAC+TGG - chr6.3:63743365-63743384 None:intergenic 30.0%
AGAGAAAAGGTAAGTAATGT+TGG - chr6.3:63743134-63743153 None:intergenic 30.0%
GGTATAAAGATAAGAATGGA+TGG + chr6.3:63743630-63743649 MS.gene065615:CDS 30.0%
TTTACCATAACAGTAAAACG+TGG + chr6.3:63743371-63743390 MS.gene065615:CDS 30.0%
! AAAATTGAGACAATTGGTTC+AGG + chr6.3:63743542-63743561 MS.gene065615:CDS 30.0%
! AACTGAAAATAACCCCTTTT+GGG + chr6.3:63743664-63743683 MS.gene065615:CDS 30.0%
! GCAATATAGTATTTTCTACC+AGG - chr6.3:63743233-63743252 None:intergenic 30.0%
! GGAAGGTATAAAGATAAGAA+TGG + chr6.3:63743626-63743645 MS.gene065615:CDS 30.0%
! GTATTTTCTACCAGGAAATA+CGG - chr6.3:63743225-63743244 None:intergenic 30.0%
! TATTTTCTACCAGGAAATAC+GGG - chr6.3:63743224-63743243 None:intergenic 30.0%
! TGTACTACAAGATTTTTCTG+AGG + chr6.3:63743325-63743344 MS.gene065615:CDS 30.0%
!! AAAAGGGGTTATTTTCAGTT+GGG - chr6.3:63743664-63743683 None:intergenic 30.0%
AGCAAAAGCTAATGGAAAGT+AGG - chr6.3:63743174-63743193 None:intergenic 35.0%
AGCTAATGGAAAGTAGGTAA+AGG - chr6.3:63743168-63743187 None:intergenic 35.0%
ATCAACGAATACAACCCAAA+AGG - chr6.3:63743681-63743700 None:intergenic 35.0%
ATTGCACCACTTATCTCTAA+AGG + chr6.3:63743248-63743267 MS.gene065615:CDS 35.0%
GAAAGTAGGTAAAGGAAAAG+AGG - chr6.3:63743160-63743179 None:intergenic 35.0%
TCAACGAATACAACCCAAAA+GGG - chr6.3:63743680-63743699 None:intergenic 35.0%
! ATTTTCTACCAGGAAATACG+GGG - chr6.3:63743223-63743242 None:intergenic 35.0%
! CAACTGAAAATAACCCCTTT+TGG + chr6.3:63743663-63743682 MS.gene065615:CDS 35.0%
!! CAAAAGGGGTTATTTTCAGT+TGG - chr6.3:63743665-63743684 None:intergenic 35.0%
!!! GATTTTTCTGAGGTTGTTAG+AGG + chr6.3:63743335-63743354 MS.gene065615:CDS 35.0%
AGTAGGTAAAGGAAAAGAGG+AGG - chr6.3:63743157-63743176 None:intergenic 40.0%
ATGATGATTTCCCTACATCC+TGG + chr6.3:63743477-63743496 MS.gene065615:CDS 40.0%
ATTATCACCAATACCTACCC+AGG - chr6.3:63743498-63743517 None:intergenic 40.0%
CAACGAATACAACCCAAAAG+GGG - chr6.3:63743679-63743698 None:intergenic 40.0%
TGATGATTTCCCTACATCCT+GGG + chr6.3:63743478-63743497 MS.gene065615:CDS 40.0%
! GACACCACGTTTTACTGTTA+TGG - chr6.3:63743378-63743397 None:intergenic 40.0%
!!! TACGGCTTTTTCAGATTCAG+TGG - chr6.3:63743705-63743724 None:intergenic 40.0%
AATGGAAACCCCGTATTTCC+TGG + chr6.3:63743212-63743231 MS.gene065615:CDS 45.0%
AGATAAGAATGGATGGCGTC+TGG + chr6.3:63743637-63743656 MS.gene065615:CDS 45.0%
AGTGTGCTGAATCTGCCAAA+TGG + chr6.3:63743444-63743463 MS.gene065615:CDS 45.0%
ATCATGAGCTAGCACCCATT+TGG - chr6.3:63743462-63743481 None:intergenic 45.0%
CAATACCTACCCAGGATGTA+GGG - chr6.3:63743490-63743509 None:intergenic 45.0%
GCGCTTGTAGTGATATTGGA+AGG + chr6.3:63743609-63743628 MS.gene065615:CDS 45.0%
GGAAAAGAGGAGGAGAGAAA+AGG - chr6.3:63743147-63743166 None:intergenic 45.0%
GGATTGAAGCTTGGTAAGAC+AGG + chr6.3:63743281-63743300 MS.gene065615:CDS 45.0%
GTGTGCTGAATCTGCCAAAT+GGG + chr6.3:63743445-63743464 MS.gene065615:CDS 45.0%
TTGGCAGATTCAGCACACTT+TGG - chr6.3:63743443-63743462 None:intergenic 45.0%
! CCACTTATCTCTAAAGGAGG+AGG + chr6.3:63743254-63743273 MS.gene065615:CDS 45.0%
! CCTCCTCCTTTAGAGATAAG+TGG - chr6.3:63743257-63743276 None:intergenic 45.0%
! CTTATCTCTAAAGGAGGAGG+TGG + chr6.3:63743257-63743276 MS.gene065615:CDS 45.0%
! GCACCACTTATCTCTAAAGG+AGG + chr6.3:63743251-63743270 MS.gene065615:CDS 45.0%
ATATCACTACAAGCGCCAGG+TGG - chr6.3:63743605-63743624 None:intergenic 50.0%
CCAATACCTACCCAGGATGT+AGG - chr6.3:63743491-63743510 None:intergenic 50.0%
CCAATATCACTACAAGCGCC+AGG - chr6.3:63743608-63743627 None:intergenic 50.0%
CCTACATCCTGGGTAGGTAT+TGG + chr6.3:63743488-63743507 MS.gene065615:CDS 50.0%
CCTGGCGCTTGTAGTGATAT+TGG + chr6.3:63743605-63743624 MS.gene065615:CDS 50.0%
GATTTCCCTACATCCTGGGT+AGG + chr6.3:63743482-63743501 MS.gene065615:CDS 50.0%
! ATCTCTAAAGGAGGAGGTGG+TGG + chr6.3:63743260-63743279 MS.gene065615:CDS 50.0%
CCATTGTTCAGTGCTCCACC+TGG + chr6.3:63743587-63743606 MS.gene065615:CDS 55.0%
!! CCAGGTGGAGCACTGAACAA+TGG - chr6.3:63743590-63743609 None:intergenic 55.0%
!! GGAGGTGGTGGATTGAAGCT+TGG + chr6.3:63743272-63743291 MS.gene065615:CDS 55.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 63743125 63743730 63743125 ID=MS.gene065615
chr6.3 mRNA 63743125 63743730 63743125 ID=MS.gene065615.t1;Parent=MS.gene065615
chr6.3 exon 63743125 63743730 63743125 ID=MS.gene065615.t1.exon1;Parent=MS.gene065615.t1
chr6.3 CDS 63743125 63743730 63743125 ID=cds.MS.gene065615.t1;Parent=MS.gene065615.t1
Gene Sequence

>MS.gene065615

ATGAAGCCAACATTACTTACCTTTTCTCTCCTCCTCTTTTCCTTTACCTACTTTCCATTAGCTTTTGCTGAAATAGTTGAAGACATAAATGGAAACCCCGTATTTCCTGGTAGAAAATACTATATTGCACCACTTATCTCTAAAGGAGGAGGTGGTGGATTGAAGCTTGGTAAGACAGGAAACTCAGACTGTCCAGTTACTGTACTACAAGATTTTTCTGAGGTTGTTAGAGGCTTGCCAGTTAGATTTACCATAACAGTAAAACGTGGTGTCATCTTTACAACTGACGAAGTAGATATTGAATTTGTTAAGAAACCAAAGTGTGCTGAATCTGCCAAATGGGTGCTAGCTCATGATGATTTCCCTACATCCTGGGTAGGTATTGGTGATAATATTGATGCATTTCAAGGTAAATTTAAAATTGAGACAATTGGTTCAGGAGCATACAAGCTTGTGTACTGTCCATTGTTCAGTGCTCCACCTGGCGCTTGTAGTGATATTGGAAGGTATAAAGATAAGAATGGATGGCGTCTGGTCCCAACTGAAAATAACCCCTTTTGGGTTGTATTCGTTGATGCCACTGAATCTGAAAAAGCCGTAGTTTGA
Protein sequence

>MS.gene065615.t1

MKPTLLTFSLLLFSFTYFPLAFAEIVEDINGNPVFPGRKYYIAPLISKGGGGGLKLGKTGNSDCPVTVLQDFSEVVRGLPVRFTITVKRGVIFTTDEVDIEFVKKPKCAESAKWVLAHDDFPTSWVGIGDNIDAFQGKFKIETIGSGAYKLVYCPLFSAPPGACSDIGRYKDKNGWRLVPTENNPFWVVFVDATESEKAVV